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https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#1
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#2
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29767704/gene-regulation-in-the-3d-genome
#3
Yun Li, Ming Hu, Yin Shen
The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In this review, we provide an overview of lessons learned from studying the chromatin structure and their implications in communications between gene promoters and distal cis-regulatory elements, such as enhancers. We first review the current knowledge of general genome organization, followed by the importance of chromatin folding in gene regulation...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29765555/a-protein-folding-molecular-imaging-biosensor-monitors-the-effects-of-drugs-that-restore-mutant-p53-structure-and-its-downstream-function-in-glioblastoma-cells
#4
Ramasamy Paulmurugan, Rayhaneh Afjei, Thillai V Sekar, Husam A Babikir, Tarik F Massoud
Misfolding mutations in the DNA-binding domain of p53 alter its conformation, affecting the efficiency with which it binds to chromatin to regulate target gene expression and cell cycle checkpoint functions in many cancers, including glioblastoma. Small molecule drugs that recover misfolded p53 structure and function may improve chemotherapy by activating p53-mediated senescence. We constructed and optimized a split Renilla luciferase (RLUC) complementation molecular biosensor (NRLUC-p53-CRLUC) to determine small molecule-meditated folding changes in p53 protein...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764984/parallel-evolution-of-common-allelic-variants-confers-flowering-diversity-in-capsella-rubella
#5
Li Yang, Hui-Na Wang, Xing-Hui Hou, Yu-Pan Zou, Ting-Shen Han, Xiao-Min Niu, Jie Zhang, Zhong Zhao, Marco Todesco, Sureshkumar Balasubramanian, Ya-Long Guo
Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' UTR region of C...
May 15, 2018: Plant Cell
https://www.readbyqxmd.com/read/29754816/the-cohesin-ring-uses-its-hinge-to-organize-dna-using-non-topological-as-well-as-topological-mechanisms
#6
Madhusudhan Srinivasan, Johanna C Scheinost, Naomi J Petela, Thomas G Gligoris, Maria Wissler, Sugako Ogushi, James E Collier, Menelaos Voulgaris, Alexander Kurze, Kok-Lung Chan, Bin Hu, Vincenzo Costanzo, Kim A Nasmyth
As predicted by the notion that sister chromatid cohesion is mediated by entrapment of sister DNAs inside cohesin rings, there is perfect correlation between co-entrapment of circular minichromosomes and sister chromatid cohesion. In most cells where cohesin loads without conferring cohesion, it does so by entrapment of individual DNAs. However, cohesin with a hinge domain whose positively charged lumen is neutralized loads and moves along chromatin despite failing to entrap DNAs. Thus, cohesin engages chromatin in non-topological, as well as topological, manners...
April 30, 2018: Cell
https://www.readbyqxmd.com/read/29748240/rec-a-like-domain-2-of-active-dna-dependent-atpase-domain-a-swi2-snf2-protein-mediates-conformational-integrity-and-atp-hydrolysis
#7
Ritu Bansal, Vijendra Arya, Ramesh Sethy, Radhakrishnan Rakesh, Rohini Muthuswami
ATP-dependent chromatin remodeling proteins use the energy released from ATP hydrolysis to reposition nucleosomes in DNA-dependent processes.  These proteins are classified as SF2 helicases. SMARCAL1, a member of this protein family, is known to modulate both DNA repair and transcription by specifically recognizing DNA molecules possessing double-strand to single-strand transition regions.  Mutations in this gene cause a rare autosomal recessive disorder known as Schimke Immuno-Osseous Dysplasia (SIOD). Structural studies have shown that the ATP-dependent chromatin remodeling proteins possess two Rec A-like domains termed as Rec A-like domain 1 and Rec A-like domain 2...
May 10, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29741584/translating-gwas-in-rheumatic-disease-approaches-to-establishing-mechanism-and-function-for-genetic-associations-with-ankylosing-spondylitis
#8
Julie A Osgood, Julian C Knight
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined...
May 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29738565/different-chromatin-and-dna-sequence-characteristics-define-glucocorticoid-receptor-binding-sites-that-are-blocked-or-not-blocked-by-coregulator-hic-5
#9
Brian H Lee, Michael R Stallcup
The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription complexes. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is necessary for glucocorticoid (GC) regulation of one group of GR target genes, is irrelevant for a second group, and inhibits GR binding to a third gene set, thereby blocking their regulation by GC...
2018: PloS One
https://www.readbyqxmd.com/read/29733521/hmga2-promotes-glioma-invasion-and-poor-prognosis-via-a-long-range-chromatin-interaction
#10
Shanshan Zhang, Huibian Zhang, Lin Yu
To identify the function and underlying mechanisms of HMGA2 on the prognosis and invasion of gliomas, HMGA2 was detected by immunohistochemistry. The Kaplan-Meier and Cox's regression analysis results showed that higher HMGA2 level predicted the poorer outcomes of glioma patients. ChIP-qPCR, DNA electrophoretic mobility shift assay, chromosome conformation capture, and co-immunoprecipitation were applied to identify HMGA2-activated target sites, which were further verified by mRNA and protein expression detection...
May 7, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29729833/compaction-of-single-molecule-megabase-long-chromatin-under-the-influence-of-macromolecular-crowding
#11
Anatoly Zinchenko, Nikolay V Berezhnoy, Qinming Chen, Lars Nordenskiöld
The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na+ and K+ ) and divalent (Mg2+ ) cations...
May 2, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29728587/cryo-em-of-nucleosome-core-particle-interactions-in-trans
#12
Silvija Bilokapic, Mike Strauss, Mario Halic
Nucleosomes, the basic unit of chromatin, are repetitively spaced along DNA and regulate genome expression and maintenance. The long linear chromatin molecule is extensively condensed to fit DNA inside the nucleus. How distant nucleosomes interact to build tertiary chromatin structure remains elusive. In this study, we used cryo-EM to structurally characterize different states of long range nucleosome core particle (NCP) interactions. Our structures show that NCP pairs can adopt multiple conformations, but, commonly, two NCPs are oriented with the histone octamers facing each other...
May 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29725103/gene-retention-fractionation-and-subgenome-differences-in-polyploid-plants
#13
REVIEW
Feng Cheng, Jian Wu, Xu Cai, Jianli Liang, Michael Freeling, Xiaowu Wang
All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality. Polyploidization has happened repeatedly in plant evolution and, we conclude, is important for crop domestication. Once duplicated, the effect of purifying selection on any one duplicated gene is relaxed, permitting duplicate gene and regulatory element loss (fractionation)...
May 2018: Nature Plants
https://www.readbyqxmd.com/read/29723572/iteratively-improving-hi-c-experiments-one-step-at-a-time
#14
Rosela Golloshi, Jacob Sanders, Rachel Patton McCord
The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases...
April 30, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29719541/a-reappraisal-on-the-potential-ability-of-human-neutrophils-to-express-and-produce-il-17-family-members-in-vitro-failure-to-reproducibly-detect-it
#15
Nicola Tamassia, Fabio Arruda-Silva, Federica Calzetti, Silvia Lonardi, Sara Gasperini, Elisa Gardiman, Francisco Bianchetto-Aguilera, Luisa Benerini Gatta, Giampiero Girolomoni, Alberto Mantovani, William Vermi, Marco A Cassatella
Neutrophils are known to perform a series of effector functions that are crucial for the innate and adaptive responses, including the synthesis and secretion of a variety of cytokines. In light of the controversial data in the literature, the main objective of this study was to more in-depth reevaluate the capacity of human neutrophils to express and produce cytokines of the IL-17 family in vitro . By reverse transcription quantitative real-time PCR, protein measurement via commercial ELISA, immunohistochemistry (IHC) and immunofluorescence (IF), flow cytometry, immunoblotting, chromatin immunoprecipitation (ChIP), and ChIP-seq experiments, we found that highly pure (>99...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29712907/theoretical-principles-of-transcription-factor-traffic-on-folded-chromatin
#16
Ruggero Cortini, Guillaume J Filion
All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables are known to influence this binding, but the distribution of transcription factor binding patterns remains mostly unexplained in metazoan genomes. Here, we investigate the role of chromosome conformation in the trajectories of transcription factors. Using molecular dynamics simulations, we uncover the principles of their diffusion on chromatin...
April 30, 2018: Nature Communications
https://www.readbyqxmd.com/read/29703667/entering-the-next-dimension-plant-genomes-in-3d
#17
REVIEW
Mariana Sotelo-Silveira, Ricardo A Chávez Montes, Jose R Sotelo-Silveira, Nayelli Marsch-Martínez, Stefan de Folter
After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but also differences, among them and with animals. The smallest structures, found in high-resolution maps of the Arabidopsis genome, are single genes...
April 24, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29691232/topological-arrangement-of-cardiac-fibroblasts-regulates-cellular-plasticity
#18
Jingyi Yu, Marcus M Seldin, Kai Fu, Shen Li, Larry Lam, Ping Wang, Yijie Wang, Dian Huang, Thang L Nguyen, Bowen Wei, Rajan P Kulkarni, Dino Di Carlo, Michael Teitell, Matteo Pellegrini, Aldons J Lusis, Arjun Deb
<u>Rationale:</u> Cardiac fibroblasts do not form a syncytium but reside in the interstitium between myocytes. This topological relationship between fibroblasts and myocytes is maintained throughout post-natal life until acute myocardial injury occurs, when fibroblasts are recruited to, proliferate and aggregate in the region of myocyte necrosis. The accumulation or aggregation of fibroblasts in the area of injury thus represents a unique event in the life cycle of the fibroblast but little is known about how changes in the topological arrangement of fibroblasts following cardiac injury affect fibroblast function...
April 24, 2018: Circulation Research
https://www.readbyqxmd.com/read/29686607/atp-dependent-chromatin-remodeling-during-cortical-neurogenesis
#19
REVIEW
Godwin Sokpor, Ricardo Castro-Hernandez, Joachim Rosenbusch, Jochen F Staiger, Tran Tuoc
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29686321/chromatin-conformation-regulates-the-coordination-between-dna-replication-and-transcription
#20
Ricardo Almeida, José Miguel Fernández-Justel, Cristina Santa-María, Jean-Charles Cadoret, Laura Cano-Aroca, Rodrigo Lombraña, Gonzalo Herranz, Alessandra Agresti, María Gómez
Chromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure, here we analyse the replication programme of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or three histone H1 genes. We find that loss of chromatin compaction in H1-depleted cells triggers the accumulation of stalled forks and DNA damage as a consequence of transcription-replication conflicts...
April 23, 2018: Nature Communications
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